Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_073039916.1 BUB04_RS12270 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_900129305.1:WP_073039916.1 Length = 296 Score = 182 bits (463), Expect = 9e-51 Identities = 114/294 (38%), Positives = 161/294 (54%), Gaps = 25/294 (8%) Query: 114 VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIA 173 V +ATL+ I ++ GLN+VVG AG + LG+ F+ +GAY ALL AG FWTALP+ Sbjct: 6 VTVATLVAIQSIVACGLNVVVGYAGQISLGHAAFFGIGAYASALLTTKAGLTFWTALPLV 65 Query: 174 GMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLF 233 + L G LLG P LR+R D+LAI T+G I+ + GG GIG IP+ T F Sbjct: 66 IAITGLVGLLLGIPSLRVRDDFLAITTIGINFIVEAVFL-YVPFFGGALGIGGIPRVTFF 124 Query: 234 GLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWE 293 + + G+ Y LY + L + L L V R G A Sbjct: 125 HVKMK--------------GLPY--------LY-LCLAFLALVLLVCRWFTRSWAGLACF 161 Query: 294 ALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILA 353 ALREDE A ++G++P KL AF +G + AG G+ +A ++ F+F S M+L+ Sbjct: 162 ALREDETAAASMGISPVRFKLLAFVLGTAMAGLGGALYAHFMRFISAGDFSFPVSVMLLS 221 Query: 354 IVVLGGMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLL 406 +VVLGGMG+ G L AV++V L E+ R E R LI+ L +++M+ ++P GLL Sbjct: 222 MVVLGGMGTLWGPTLGAVILVSLPELFRPLLEIRFLIYTLLLLLMIRFQPGGLL 275 Lambda K H 0.330 0.146 0.439 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 355 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 296 Length adjustment: 29 Effective length of query: 388 Effective length of database: 267 Effective search space: 103596 Effective search space used: 103596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory